I have seen a yacht club rescue RIB transom crudely built up with timber to prevent this. I guess you could build up the transom either side of the engine. (Mine has a sort of "notch" where the engine is fitted and rises up to where the tubes are.)
I am guessing the "pooping" effect is from waves whilst stationary & diving? You are not getting swamped by your own wash are you? If so the don't slow down so suddenly
Apart from that, fit the biggest electric bilge pump you can to clear the water as fast as possible!